Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 29

System / cell line: populations ✕ Assay: inference ✕ Clear

Direct maximum parsimony phylogeny reconstruction from genotype data.

PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

simulated mitochondrial lipoprotein coalescent maximum sliding-window
Inferring human colonization history using a copying model.

PMID 18497854 · PMC2367454 · PLoS genetics · 2008 · 8 claims · 6 setups

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A copying-model approach using SNP haplotype sharing can infer both the order of population founding and the donor populations contributing ancestry to each new population.

simulated populations coalescent snp ascertainment
Tracing human genetic histories and natural selection with precise local ancestry inference.

PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

Has reproduction · 76

Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

1kgp-16pops independent simulated 1kgp simulated population-level local
GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline.

PMID 33193602 · PMC7541957 · Frontiers in genetics · 2020 · 7 claims · 4 setups

Has reproduction · 80

GenomeChronicler is the first pipeline able to run offline or in the cloud to generate personal genomics reports (not limited to disease) from whole genome or whole exome sequencing data.

wgs na12878 pgp-uk1 genomes ancestry germline genome
Cis-regulatory evolution shapes facial diversity in birds and mammals.

PMID 42090501 · PMC13148318 · Science advances · 2026 · 8 claims · 6 setups

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Mesenchymal populations show markedly greater transcriptomic/regulatory divergence between mouse and chicken than ectodermal populations, pointing to a central role of mesenchyme in shaping facial morphology

embryo chicken embryos single-cell situ cross-species
The origins of lactase persistence in Europe.

PMID 19714206 · PMC2722739 · PLoS computational biology · 2009 · 8 claims · 5 setups

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The −13,910*T allele first underwent selection among dairying farmers around 7,500 years ago in a region between the central Balkans and central Europe, possibly linked to the Linearbandkeramik culture.

simulated simulation 910*t farming demic approximate comparison
scDock: streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

PMID 41769845 · PMC12996892 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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scDock is an integrated pipeline connecting scRNA-seq processing, cell-cell communication inference, and molecular docking-based drug discovery through a single configuration file

diabetic kidney ppia glimepiride-ppia scrna-seq cell-cell type
Pulmonary organoid models demonstrate compositionally driven epithelial plasticity and immune polarization.

PMID 41940331 · PMC13049529 · iScience · 2026 · 8 claims · 7 setups

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Cellular composition at seeding (PD vs. BAL vs. Mixed) directs epithelial fate and immune polarization in organoid culture

lung day organoid epithelial scrna-seq brightfield h&e
Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.

PMID 41540084 · PMC12894745 · NPJ systems biology and applications · 2026 · 8 claims · 8 setups

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The presence of immune cells in the environment significantly alters CLL cell activation

autologous monoculture non-adherent pbmc bulk flow deconvolution
The genome landscape of Hong Kong feral cattle as a unique genetic resource.

PMID 42006315 · PMC13091034 · iScience · 2026 · 8 claims · 8 setups

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HKF cattle harbor high genetic diversity despite a declining effective population size, indicating untapped genetic potential

hkf autosomal wgs whole-genome pca runs
Charting spatial ligand-target activity using Renoir.

PMID 42086556 · PMC13144314 · Nature communications · 2026 · 8 claims · 8 setups

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Renoir computes a neighborhood activity score for curated ligand-target pairs at each spatial spot/cell by integrating cell type abundance, cell type-specific mRNA abundance, receptor expression, gene entropy, and mutual information between ligand and target genes.

intestine triple-negative dorsolateral dlpfc semi-synthetic spatial single-cell
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

PMID 30951143 · PMC6450036 · Database : the journal of biological databases and curation · 2019 · 7 claims · 7 setups

Has reproduction · 80

PanglaoDB is a web server providing pre-processed and pre-computed analyses of published mouse and human scRNA-seq experiments through a user-friendly interface.

randomly single-cell single scrna-seq cell-type orthogonal
Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

Has reproduction · 81

scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell
Developmental dynamics of catshark cranial neural crest cells provide insights into gnathostome facial evolution.

PMID 41987760 · PMC13200729 · Development (Cambridge, England) · 2026 · 8 claims · 8 setups

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The molecular toolkit of CNCCs is largely conserved across jawed vertebrates (gnathostomes)

scyliorhinus catshark chicken immunofluorescence single-cell umap
Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

PMID 19859740 · PMC2939908 · Human genetics · 2010 · 7 claims · 7 setups

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NOS2 promoter haplotypes are not consistently associated with malaria severity or malarial anemia across three independent Tanzanian study populations

tanzanian a549 muheza-tanga sscp pcr restriction
Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

PMID 42063567 · PMC13127482 · iScience · 2026 · 8 claims · 8 setups

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LUSC arising within UIP originates from AT2-derived metaplastic basal cells

fresh-frozen same scrna-seq paired single-cell copy ligand-receptor
Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

PMID 18304320 · PMC2292740 · BMC genetics · 2008 · 8 claims · 8 setups

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NAT2 coding region sequence variation in the Mandenka and other sub-Saharan African populations is consistent with selective neutrality and constant population size.

mandenka worldwide hapmap nat2 full snp analysis
The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes.

PMID 41671394 · PMC12951522 · Genome biology and evolution · 2026 · 8 claims · 8 setups

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Gouania slender and stout morphotypes evolved convergently at least twice within the genus, confirmed by 3D morphometrics and phylogenomics

pelvic individuals draft gouania geometric barcoding phylogenomics
Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).

PMID 35444631 · PMC9014210 · Frontiers in microbiology · 2022 · 7 claims · 7 setups

Has reproduction · 55

The gut microbiome of C. fluminea is diverse, differs with environmental conditions, and varies spatially among rivers, but is unrelated to host genetic variation

corbicula six sediment filtered 16s radseq picrust2
Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.

PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

Has reproduction · 23

Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations

newly duck southeast chinese whole-genome phylogenetic population

Experiments

Direct maximum parsimony phylogeny reconstruction from genotype data.

Inferring human colonization history using a copying model.

Tracing human genetic histories and natural selection with precise local ancestry inference.

GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline.

Cis-regulatory evolution shapes facial diversity in birds and mammals.

The origins of lactase persistence in Europe.

scDock: streamlining drug discovery targeting cell-cell communication via scRNA-seq analysis and molecular docking.

Pulmonary organoid models demonstrate compositionally driven epithelial plasticity and immune polarization.

Data driven network inference and longitudinal transcriptomics unveil dynamic regulation in Chronic Lymphocytic Leukaemia models.

The genome landscape of Hong Kong feral cattle as a unique genetic resource.

Charting spatial ligand-target activity using Renoir.

PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data.

Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

Developmental dynamics of catshark cranial neural crest cells provide insights into gnathostome facial evolution.

Malaria severity and human nitric oxide synthase type 2 (NOS2) promoter haplotypes.

Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

The Genomics of Convergent Adaptation to Intertidal Gravel Beaches in Mediterranean Clingfishes.

Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).

Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.